rs10751331

chr10-43648025-G-Achr10-43648025-G-Cchr10-43648025-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006973.3(ZNF32):c.-70+777C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,998 control chromosomes in the GnomAD database, including 9,329 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.34 (9329 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF32 NM_006973.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

Genes affected

ZNF32 (HGNC:13095): (zinc finger protein 32) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF32-AS3 (HGNC:23583): (ZNF32 antisense RNA 3)

ZNF32-AS2 (HGNC:23593): (ZNF32 antisense RNA 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF32	NM_006973.3	c.-70+777C>T		intron_variant		ENST00000374433.7
ZNF32-AS3	NR_038867.1	n.162+19047G>A		intron_variant, non_coding_transcript_variant
ZNF32-AS2	NR_047558.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF32	ENST00000374433.7	c.-70+777C>T		intron_variant		1	NM_006973.3	P1
ZNF32-AS3	ENST00000458063.1	n.162+19047G>A		intron_variant, non_coding_transcript_variant		1
ZNF32	ENST00000395797.1	c.-70+560C>T		intron_variant		2		P1
ZNF32-AS2	ENST00000418966.1			downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51724 AN: 151880 Hom.: 9326 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.331

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.340 AC: 51750 AN: 151998 Hom.: 9329 Cov.: 32 AF XY: 0.345 AC XY: 25616 AN XY: 74336

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.328

Alfa AF: 0.282 Hom.: 1897

Bravo AF: 0.347

Asia WGS AF: 0.491 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	14
Dann	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10751331; hg19: chr10-44143473;